[aroma.affymetrix] Re: Re-run aroma.affymetrix

Hi Anbarasu. Comments below. Hi Mark, Thanks for your suggestions. What I have tried so far is: I removed all outliers CEL files from rawData and re-run the analysis. I was expecting a slightly different intensity distributions of chips (due to quantile normalization) but it seems I have

[aroma.affymetrix] Re: RMA of aroma.affymetrix, affyPLM and affy

Hi Yiwen. I think this thread will answer your question in detail: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/1b0ab11fad9b4df3 In brief, the main difference is how the probe-level linear model is fit -- median polish OR iteratively reweighted least squares with a